Legumes are indispensable for human diet in respect to their valuable and nutritive bioactive molecules. Legumes and derivative foodstuffs are rich in fiber, proteins, vitamins and some valuable phytochemicals, which exhibit important biological activities. Due to their remarkable molecular content, they are receiving great attention by researchers. Recent developments in genomics and bioinformatics led to cumulative data about legume genomes. These data could provide important information to accelerate breeding and to develop new traits for biofortification. The main focus of this review is to present their distinctive genomic properties by summarizing significant studies conducted with relatively newly developed techniques revealing the beneficial effects of bioactive molecules from legumes on human health.